Overview

The ATOM records present the atomic coordinates for standard residues (see http://deposit.pdb.org/public-component-erf.cif). They also present the occupancy and temperature factor for each atom. Heterogen coordinates use the HETATM record type. The element symbol is always present on each ATOM record; segment identifier and charge are optional.

If more than one model is present in the entry, each model is delimited by MODEL and ENDMDL records.

If an atom is provided in more than one position, then a non-blank alternate location indicator must be used as the alternate location indicator for each of the positions. Within a residue all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator.

For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/ HETATM list uses the following general rules:

In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry.

In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together.

The insertion code is commonly used in sequence numbering

If the depositor provides the data, then the isotropic B value is given for the temperature factor.

If there are neither isotropic B values from the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.

Columns 79 - 80 indicate any charge on the atom, e.g., 2+, 1-. In most cases these are blank.

Verification/Validation/Value Authority Control

PDB checks ATOM/HETATM records for PDB format, sequence information, and packing. The PDB reserves the right to return deposited coordinates to the author for transformation into PDB format.

Relationships to Other Record Types

The ATOM records are compared to the corresponding sequence database. Residue discrepancies appear in the SEQADV record. Missing atoms are annotated in the remarks. HETATM records are formatted in the same way as ATOM records. The sequence implied by ATOM records must be identical to that given in SEQRES, with the exception that residues that have no coordinates, e.g., due to disorder, must appear in SEQRES.